Avoid Manila. It is one of the world’s most heavily polluted, dangerous and ugly cities. The streets reek with bad attitude and your mood deteriorates with each hour you spend there. The buildings are all falling down (except the wealthy homes and shopping malls which are immaculately American) and the virus of American consumer culture and corporate greed has posinoed this city.
If you do get stuck here for a night for some inexplicable reason and you want to see how bad it can get, Makati is the main nightlife district and has all the skyscrapers and red light zones. It is very dangerous and some sources claim that twenty people are murdered in just this part of town every night.
There is no real central bus station, so just do the best you can to figure out how to get out of this megalopolis of more than 12 million people. Metered taxis are pretty cheap and safer than jeepneys.
Trying to figure out a bus route through Manila is difficult, but since most people speak English, it can be done. Watch your wallet at all times. Ask for “Superferry” to take the large ferries to different islands.